134 lines
4.0 KiB
Java
134 lines
4.0 KiB
Java
package org.gcube.data.spd.catalogueoflife.capabilities;
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import java.io.IOException;
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import java.io.InputStream;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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import javax.xml.namespace.QName;
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import javax.xml.stream.XMLEventReader;
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import javax.xml.stream.XMLInputFactory;
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import javax.xml.stream.XMLStreamException;
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import javax.xml.stream.events.Attribute;
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import javax.xml.stream.events.StartElement;
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import javax.xml.stream.events.XMLEvent;
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import org.gcube.data.spd.catalogueoflife.CatalogueOfLifePlugin;
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import org.gcube.data.spd.catalogueoflife.Utils;
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import org.gcube.data.spd.model.exceptions.StreamNonBlockingException;
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import org.gcube.data.spd.plugin.fwk.capabilities.ExpansionCapability;
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import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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public class ExpansionCapabilityImpl implements ExpansionCapability {
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static Logger logger = LoggerFactory.getLogger(ExpansionCapabilityImpl.class);
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@Override
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public void getSynonyms(ObjectWriter<String> writer, String scientifcName) {
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getIds(scientifcName, 0, writer);
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}
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//recorvise method to get a list of ids by scientific name
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private List<String> getIds(String scientifcName, int start, ObjectWriter<String> writer) {
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String pathUrl = CatalogueOfLifePlugin.baseurl + "?name=" + scientifcName.replaceAll(" ", "+") + "*&response=full&start=" + start;
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// logger.trace("PATH " + pathUrl);
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int total_number_of_results = 0;
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int number_of_results_returned = 0;
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List<String> ids = new ArrayList<String>();
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InputStream is = null;
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XMLInputFactory ifactory;
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XMLEventReader eventReader = null;
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try{
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is = URI.create(pathUrl).toURL().openStream();
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ifactory = XMLInputFactory.newInstance();
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eventReader = ifactory.createXMLEventReader(is);
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while (eventReader.hasNext()){
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XMLEvent event = eventReader.nextEvent();
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if (Utils.checkStartElement(event, "results")){
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StartElement element = (StartElement) event;
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@SuppressWarnings("unchecked")
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Iterator<Attribute> iterator = element.getAttributes();
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while (iterator.hasNext()) {
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Attribute attribute = (Attribute) iterator.next();
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QName att = attribute.getName();
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if (att.toString().equals("total_number_of_results")){
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total_number_of_results = (Integer.parseInt(attribute.getValue()));
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}
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else if (att.toString().equals("number_of_results_returned")){
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number_of_results_returned = (Integer.parseInt(attribute.getValue()));
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}
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}
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continue;
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}
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else if (Utils.checkStartElement(event, "synonyms")){
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readSynonyms(eventReader, writer);
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continue;
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}
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else if (Utils.checkEndElement(event, "results")){
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if (total_number_of_results > number_of_results_returned + start)
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getIds(scientifcName, start+50, writer);
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else
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break;
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}
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}
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} catch (Exception e) {
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writer.write(new StreamNonBlockingException("CatalogueOfLife",""));
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}finally{
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try {
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if (eventReader != null)
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eventReader.close();
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if (is != null)
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is.close();
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} catch (XMLStreamException e) {
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logger.error("XMLStreamException",e);
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} catch (IOException e) {
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logger.error("IOException",e);
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}
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}
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return ids;
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}
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//read from <synonyms> to </synonyms>
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private void readSynonyms(XMLEventReader eventReader, ObjectWriter<String> writer) throws XMLStreamException {
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while (eventReader.hasNext()){
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XMLEvent event = eventReader.nextEvent();
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if (Utils.checkStartElement(event, "synonym")){
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while (eventReader.hasNext()){
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event = eventReader.nextEvent();
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if (Utils.checkStartElement(event, "name")){
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event = eventReader.nextEvent();
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if (event.isCharacters()){
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String id = event.asCharacters().getData();
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// System.out.println(id);
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if (!writer.isAlive()) return;
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writer.write(id);
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}
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}
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else if (Utils.checkEndElement(event, "synonym"))
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break;
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}
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}
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else if (Utils.checkEndElement(event, "synonyms"))
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break;
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}
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}
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}
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